A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets.

Ángel F Álvarez-Prado,Arantxa Pérez-García,Alberto Benguria,Almudena R Ramiro,Carlos Torroja,Virginia G De Yébenes,Pablo Pérez-Durán

doi:10.1084/jem.20171738

Abstract

Activation-induced deaminase (AID) initiates antibody diversification in germinal center (GC) B cells through the deamination of cytosines on immunoglobulin genes. AID can also target other regions in the genome, triggering mutations or chromosome translocations, with major implications for oncogenic transformation. However, understanding the specificity of AID has proved extremely challenging. We have sequenced at very high depth >1,500 genomic regions from GC B cells and identified 275 genes targeted by AID, including 30 of the previously known 35 AID targets. We have also identified the most highly mutated hotspot for AID activity described to date. Furthermore, integrative analysis of the molecular features of mutated genes coupled to machine learning has produced a powerful predictive tool for AID targets. We also have found that base excision repair and mismatch repair back up each other to faithfully repair AID-induced lesions. Finally, our data establish a novel link between AID mutagenic activity and lymphomagenesis.

Highlights

Activation-induced deaminase (AID) is a crucial enzyme for the immune response because it generates high-affinity and switched antibodies in germinal center (GC) B cells by somatic hypermutation (SHM) and class switch recombination (CSR; Muramatsu et al, 2000; Revy et al, 2000)
Capture-based deep sequencing allows high-throughput identification of AID targets To explore the scope of AID-induced mutations at a highthroughput scale, we designed a capture library against 1,588 regions corresponding to 1,379 different genes as a representation of the B cell genome (Table S1; see Design of DNA capture library in the Materials and methods).Genomic DNA from GC B cells was isolated, captured, and deep sequenced (Fig. S1, A and B).We made use of a mouse model deficient for both base excision repair (BER) and mismatch repair (MMR) pathways (Ung−/−Msh2−/− mice)
We found a set of 291 genomic regions that were reproducibly mutated in Ung−/−Msh2−/− GC B cells when compared with Aicda−/− GC B cells (q ≤ 0.05; Fig. 1 A; Fig. S1, C–E; and Table S2; representative targets were validated by Sanger sequencing; Fig. 1 B and Table S3)

Summary

Introduction

Activation-induced deaminase (AID) is a crucial enzyme for the immune response because it generates high-affinity and switched antibodies in germinal center (GC) B cells by somatic hypermutation (SHM) and class switch recombination (CSR; Muramatsu et al, 2000; Revy et al, 2000). RESULTS AND DISCUSSION Capture-based deep sequencing allows high-throughput identification of AID targets To explore the scope of AID-induced mutations at a highthroughput scale, we designed a capture library against 1,588 regions corresponding to 1,379 different genes as a representation of the B cell genome (Table S1; see Design of DNA capture library in the Materials and methods).Genomic DNA from GC B cells was isolated, captured, and deep sequenced (Fig. S1, A and B).We made use of a mouse model deficient for both BER and MMR pathways (Ung−/−Msh2−/− mice).

Results

Conclusion